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        Note that additional data was saved in multiqc_data when this report was generated.

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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        Tool Citations

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        About MultiQC

        This report was generated using MultiQC, version 1.21

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2024-05-23, 11:00 EDT based on data in: /scr/dings/PEVO/22_DNA_gencode_ref_new2/anne_vep/annotated

        General Statistics

        Showing 1/1 rows and 3/3 columns.
        Sample NameChange rateTs/TvM Variants
        chr1.imputed.poly_subset
        2495
        2.431
        0.10M

        SnpEff

        Version: 5.2

        SnpEff is a genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes). .DOI: 10.4161/fly.19695.

        Variants by Genomic Region

        The stacked bar plot shows locations of detected variants in the genome and the number of variants for each location.

        The upstream and downstream interval size to detect these genomic regions is 5000bp by default.

        Created with MultiQC

        Variant Effects by Impact

        The stacked bar plot shows the putative impact of detected variants and the number of variants for each impact.

        There are four levels of impacts predicted by SnpEff:

        • High: High impact (like stop codon)
        • Moderate: Middle impact (like same type of amino acid substitution)
        • Low: Low impact (ie silence mutation)
        • Modifier: No impact
        Created with MultiQC

        Variants by Effect Types

        The stacked bar plot shows the effect of variants at protein level and the number of variants for each effect type.

        This plot shows the effect of variants with respect to the mRNA.

        Created with MultiQC

        Variants by Functional Class

        The stacked bar plot shows the effect of variants and the number of variants for each effect type.

        This plot shows the effect of variants on the translation of the mRNA as protein. There are three possible cases:

        • Silent: The amino acid does not change.
        • Missense: The amino acid is different.
        • Nonsense: The variant generates a stop codon.
        Created with MultiQC

        VEP

        VEP Ensembl VEP determines the effect of your variants on genes, transcripts and protein sequences, as well as regulatory regions.DOI: 10.1186/s13059-016-0974-4.

        General Statistics

        Table showing general statistics of VEP annotaion run

        Showing 1/1 rows and 5/6 columns.
        Sample NameOverlapped regulatory featuresOverlapped transcriptsOverlapped genesVariants filtered outVariants processed
        chr1.imputed.poly_subset
        0
        2007
        565
        0
        99933

        Variant classes

        Classes of variants found in the data.

        Created with MultiQC

        Consequences

        Predicted consequences of variations.

        Created with MultiQC

        Variants by chromosome

        Number of variants found on each chromosome.

        Created with MultiQC

        Position in protein

        Relative position of affected amino acids in protein.

        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        SoftwareVersion
        SnpEff5.2

        MultiQC v1.21 - Written by Phil Ewels, available on GitHub.

        This report uses HighCharts, jQuery, jQuery UI, Bootstrap, FileSaver.js and clipboard.js.